Has the continuity timeline been established for the new X-men movies?

I'm not sure how there's any confusion about Professor X being in the wheelchair. He's clearly "shot" (bullet deflected) in the First Class movie, as well as being IN the wheelchair at the end.

As for Emma's story, there was a lot of confusion about the character thanks to the Wolverine: Origins movie. There's a young girl being held captive by Stryker who can turn into diamond. Many believed that she was Emma, yet she's only referred to as "Kayla's sister", even in the credits. It is possible they could make that reference in future movies, or not.

With regards to Sabertooth and Wolverine's "relationship", that will be a bit easier to do. Since Wolverine lost his memory, he has no idea why Sabertooth seems to be hunting him. In the comics, Sabertooth hunts him down every year on his birthday, just to beat him to a pulp. This is to show that he's always going to be the superior mutant. If I recall, to this day, Wolverine has not beaten Sabertooth in a one on one.

Now, as for potential issues that could arise, there's one that comes to my mind. If Wolverine does make an appearance in this film, much more than the cameo we saw in First Class, why does Professor X seemingly have no knowledge of him in X-Men? Wolverine's lack of memory is understandable, as we know that Wolverine: Origins takes place quite some time before First Class, and thus he's lost his memory.

Ultimately, though, the sad answer is that they will "try" to address what they think needs addressing and nothing more. The hope is that if there are any glaring holes, they'll fix these. But it's really up to the director and the writers to pay attention and try to make it mesh as seamlessly as possible.

As per the movie name says X-Men: Days of Future Past which it sounds similar to Days of Future Past comics storyline and as per the confirmed cast of Hugh Jackman, Ian Mckellen, Patrick Stewart, Anna Paquin, Shawn Ashmore, Ellen Page, Michael Fassbender, Nicholas Hoult, Jennifer Lawrence, and James McAvoy, it is clear that they are making it a midequel between X-Men new class and X-men trilogy. Its very difficult to connect it to Walvoreine

The upcoming The Wolverine(2013) is intended to be a stand-alone film, taking place after the events of X-Men: The Last Stand.

Producer Lauren Shuler Donner reported in August 2006 that renegotiations would be required to continue the main film series. Newer cast members were signed, while the older cast members, including Halle Berry, Rebecca Romijn, Famke Janssen, and Anna Paquin, were not. Donner admitted, "There is forty years worth of stories. I’ve always wanted to do 'Days of Future Past' and there are just really a lot of stories yet to be told." She later pitched Bryan Singer on doing a fourth installment of the previously established X-Men franchise, following the completion of X-Men: First Class. In March 2011, Shuler Donner revealed that the film was in "active development at Fox," saying, "We took the treatment to Fox and they love it... And X4 leads into X5". In October 2012, Donner expressed interest in having the X-Men characters appear in Marvel Studios' independently produced Marvel Cinematic Universe films. Shuler Donner said, "I would love it. I personally have close ties to Marvel because of Kevin Feige, because Kevin worked for me. But to take our characters and mingle them in the way that they were written, yeah, absolutely.(source)

X-Men: Days of Future Past (2014)

To be directed by Bryan Singer, the film will feature the cast of X-Men: First Class along with the some of the cast from the original X-Men trilogy. Set in 1973, 10 years after X-Men: First Class, the film features a script from Simon Kinberg and is said to be inspired by Chris Claremont and John Byrne's X-Men comic book storyline, "Days of Future Past". Matthew Vaughn was supposed to direct the film but left the director duties to focus on Mark Millar's The Secret Service film adaptation. Vaughn will still be attached to the film writing alongside Kinberg and producing. Confirmed cast members for the film include James McAvoy, Michael Fassbender, Jennifer Lawrence, Nicholas Hoult, Patrick Stewart, Ian McKellen, Hugh Jackman, Anna Paquin, Ellen Page, and Shawn Ashmore. The film is scheduled to go into production in April 2013, and is scheduled to be released on 18 July 2014.

Even Fox's upcoming reboot of the Fantastic Four film series will share continuity with the X-Men series, creating a shared universe similar to the Marvel Cinematic Universe produced by Marvel Studios.(source)?